5TH4

Crystal Structure of 1-hydroxypyridine-2(1H)-thione bound to human carbonic anhydrase 2 L198G


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KS3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8291Ammonium Sulfate, Tris, pH 8.0, VAPOR DIFFUSION, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.1141.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.2α = 90
b = 41.333β = 104.65
c = 72.159γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 60002015-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR5911.5478

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.4269.8194.70.045119.85.7543001
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.421.4743.30.58160.771820

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3KS31.474038622206398.710.182450.180850.21184RANDOM15.888
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.30.08-0.23-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.415
r_dihedral_angle_4_deg24.858
r_dihedral_angle_3_deg14.564
r_dihedral_angle_1_deg7.011
r_long_range_B_refined5.397
r_scbond_it3.167
r_mcangle_it2.516
r_angle_refined_deg2.432
r_mcbond_it1.759
r_chiral_restr0.167
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.415
r_dihedral_angle_4_deg24.858
r_dihedral_angle_3_deg14.564
r_dihedral_angle_1_deg7.011
r_long_range_B_refined5.397
r_scbond_it3.167
r_mcangle_it2.516
r_angle_refined_deg2.432
r_mcbond_it1.759
r_chiral_restr0.167
r_bond_refined_d0.025
r_gen_planes_refined0.016
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2045
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms19

Software

Software
Software NamePurpose
REFMACrefinement
APEXdata collection
PHASERphasing